The issue is Marvel Studios isn't connected technically to Marvel Comics, they don't have any pull on what they do in the films. Marvel Comics is a division of the larger Marvel Entertainment like Marvel Games is now, whereas Marvel Studios is a direct subsidiary of The Walt Disney Company separate from the Comic publishing company and Marvel Entertainment as of like 2015 I think. They're more like sister companies and this makes connections going forward a little more difficult.
Now again you're 100% the MCU is part of the comics Multiverse because the comics say so, that's just a fact there's connections between the two. The issue is how none of the connections come right from Marvel Studios projects, it's all through something else like how Pro Bot pointed out the Insomiac Comic Spider-Man mentioned Spider-Geddon and he was in AtSV which mentioned the MCU therefore they are connected, they're not wrong. But from the MCU's end they're specifically making distinctions between them. Now again I want to make it clear I'm not saying the MCU isn't part of the Marvel Comics Multiverse, I'm saying in the future if Marvel Studios continues this way they'll likely cause more contradictions than connections and that can make things difficult.
Right now there's nothing that can't be spun to easily say they're still part of the same Multiverse. However when two different companies are making products set in the same multiverse and one actively seems to want to retcon themselves out of that multiverse eventually it could happen. And the thing some people don't get is Marvel Studios is not under Marvel Entertainment or Marvel Comics and if they choose to separate themselves from the Comic Multiverse officially they absolutely can. I'm not saying they have or they will, just that they've made some suspicious choices and the connections to the Comics Multiverse are very one sided.
TL;DR Yeah they're connected but saying Marvel Comics/Entertainment > Marvel Studios is incorrect and if Marvel Studios says otherwise Marvel Comics couldn't say they're wrong cause the MCU isn't their product.